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Fix lims sarscov2 test #4111

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merged 1 commit into from
Jan 17, 2025
Merged

Fix lims sarscov2 test #4111

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16 changes: 8 additions & 8 deletions tests/fixtures/cgweb_orders/sarscov2.json
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Original file line number Diff line number Diff line change
Expand Up @@ -36,20 +36,20 @@
"lab_code": null,
"mother": null,
"name": "sarscov2sample1",
"organism": "other",
"organism_other": "unknown",
"original_lab": "Unilabs Stockholm",
"original_lab_address": "171 54 Solna",
"organism": "SARS-CoV-2",
"organism_other": "",
"original_lab": "Karolinska University Hospital Solna",
"original_lab_address": "171 76 Solna",
"phenotype_groups": null,
"phenotype_terms": null,
"pool": null,
"post_formalin_fixation_time": null,
"pre_processing_method": "Other (specify in \"Comments\")",
"pre_processing_method": "COVIDSeq",
"primer": "Illumina Artic V3",
"priority": "research",
"quantity": "3",
"reagent_label": null,
"reference_genome": "NC_000001",
"reference_genome": "NC_111",
"region": "Stockholm",
"region_code": "01",
"require_qc_ok": null,
Expand Down Expand Up @@ -331,8 +331,8 @@
"lab_code": null,
"mother": null,
"name": "sarscov2sample6",
"organism": "SARS-CoV-2",
"organism_other": "",
"organism": "other",
"organism_other": "unknown",
"original_lab": "LaboratorieMedicinskt Centrum Gotland",
"original_lab_address": "621 84 Visby",
"phenotype_groups": null,
Expand Down
16 changes: 7 additions & 9 deletions tests/services/orders/lims_service/test_order_lims_service.py
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Original file line number Diff line number Diff line change
Expand Up @@ -144,17 +144,15 @@ def test_to_lims_microbial(microbial_order_to_submit: dict):
assert first_sample["udfs"]["volume"] == "20"


@pytest.mark.xfail(reason="Mutant extraction methods need a new enum")
def test_to_lims_sarscov2(sarscov2_order_to_submit: dict):
def test_to_lims_sarscov2(mutant_order: MutantOrder):
# GIVEN a sarscov2 order for samples
order_data = MutantOrder.model_validate(sarscov2_order_to_submit)

# WHEN parsing for LIMS
samples: list[LimsSample] = OrderLimsService._build_lims_sample(
customer="cust000",
samples=order_data.samples,
samples=mutant_order.samples,
workflow=Workflow.MUTANT,
delivery_type=order_data.delivery_type,
delivery_type=mutant_order.delivery_type,
)

# THEN it should have found the same number of samples
Expand All @@ -164,16 +162,16 @@ def test_to_lims_sarscov2(sarscov2_order_to_submit: dict):
assert first_sample["udfs"]["collection_date"] == "2021-05-05"
assert first_sample["udfs"]["extraction_method"] == "MagNaPure 96"
assert first_sample["udfs"]["lab_code"] == "SE100 Karolinska"
assert first_sample["udfs"]["organism"] == "SARS CoV-2"
assert first_sample["udfs"]["organism"] == "SARS-CoV-2"
assert first_sample["udfs"]["original_lab"] == "Karolinska University Hospital Solna"
assert first_sample["udfs"]["original_lab_address"] == "171 76 Stockholm"
assert first_sample["udfs"]["original_lab_address"] == "171 76 Solna"
assert first_sample["udfs"]["pre_processing_method"] == "COVIDSeq"
assert first_sample["udfs"]["priority"] == "research"
assert first_sample["udfs"]["reference_genome"] == "NC_111"
assert first_sample["udfs"]["region"] == "Stockholm"
assert first_sample["udfs"]["region_code"] == "01"
assert first_sample["udfs"]["selection_criteria"] == "1. Allmän övervakning"
assert first_sample["udfs"]["volume"] == "1"
assert first_sample["udfs"]["selection_criteria"] == "Allmän övervakning"
assert first_sample["udfs"]["volume"] == "20"


def test_to_lims_balsamic(balsamic_order_to_submit: dict):
Expand Down
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